Merge pull request #216 from linkml/linkml-issue-1023

Handle any_of of ranges in rdflib_loader

linkml_runtime/loaders/rdflib_loader.py

@@ -126,14 +126,17 @@ def from_rdf_graph(self, graph: Graph, schemaview: SchemaView, target_class: Typ
                                 logging.debug(f'No CURIE for {p}={o} in {subject} [{subject_class}]')
                                 v = str(o)
                         elif EnumDefinition.class_name in range_applicable_elements:
+                            range_union_elements = schemaview.slot_range_as_union(slot)
+                            enum_names = [e for e in range_union_elements if e in schemaview.all_enums()]
                             # if a PV has a meaning URI declared, map this
                             # back to a text representation
                             v = namespaces.curie_for(o)
-                            e = schemaview.get_enum(slot.range)
-                            for pv in e.permissible_values.values():
-                                if v == pv.meaning or str(o) == pv.meaning:
-                                    v = pv.text
-                                    break
+                            for enum_name in enum_names:
+                                e = schemaview.get_enum(enum_name)
+                                for pv in e.permissible_values.values():
+                                    if v == pv.meaning or str(o) == pv.meaning:
+                                        v = pv.text
+                                        break
                         elif TypeDefinition.class_name in range_applicable_elements:
                             if cast_literals:
                                 v = namespaces.curie_for(o)

tests/test_loaders_dumpers/input/personinfo.yaml

@@ -72,6 +72,7 @@ classes:
       - current_address
       - has_employment_history
       - has_familial_relationships
+      - has_interpersonal_relationships
       - has_medical_history
     slot_usage:
       primary_email:
@@ -188,6 +189,18 @@ classes:
         range: Person
         required: true
 
+  InterPersonalRelationship:
+    is_a: Relationship
+    slot_usage:
+      type:
+        any_of:
+          - range: FamilialRelationshipType
+          - range: NonFamilialRelationshipType
+        required: true
+      related to:
+        range: Person
+        required: true
+
   EmploymentEvent:
     is_a: Event
     slots:
@@ -253,6 +266,10 @@ slots:
     range: FamilialRelationship
     multivalued: true
     inlined_as_list: true
+  has_interpersonal_relationships:
+    range: InterPersonalRelationship
+    multivalued: true
+    inlined_as_list: true
   in location:
     range: Place
   current_address:
@@ -318,6 +335,14 @@ enums:
         meaning: famrel:02
       CHILD_OF:
         meaning: famrel:01
+  NonFamilialRelationshipType:
+    permissible_values:
+      COWORKER_OF:
+        meaning: famrel:70
+      ROOMMATE_OF:
+        meaning: famrel:71
+      BEST_FRIEND_OF:
+      MORTAL_ENEMY_OF:
   GenderType:
     permissible_values:
       nonbinary man:
@@ -345,3 +370,4 @@ enums:
       shell company:
       loose organization:
 
+

tests/test_loaders_dumpers/models/personinfo.py

@@ -1,5 +1,5 @@
 # Auto generated from personinfo.yaml by pythongen.py version: 0.9.0
-# Generation date: 2021-12-26T18:13:04
+# Generation date: 2022-10-19T17:57:17
 # Schema: personinfo
 #
 # id: https://w3id.org/linkml/examples/personinfo
@@ -26,6 +26,7 @@
 from linkml_runtime.utils.metamodelcore import Bool, Decimal, URI, URIorCURIE, XSDDate
 
 metamodel_version = "1.7.0"
+version = None
 
 # Overwrite dataclasses _init_fn to add **kwargs in __init__
 dataclasses._init_fn = dataclasses_init_fn_with_kwargs
@@ -169,6 +170,7 @@ class Person(NamedThing):
     current_address: Optional[Union[dict, "Address"]] = None
     has_employment_history: Optional[Union[Union[dict, "EmploymentEvent"], List[Union[dict, "EmploymentEvent"]]]] = empty_list()
     has_familial_relationships: Optional[Union[Union[dict, "FamilialRelationship"], List[Union[dict, "FamilialRelationship"]]]] = empty_list()
+    has_interpersonal_relationships: Optional[Union[Union[dict, "InterPersonalRelationship"], List[Union[dict, "InterPersonalRelationship"]]]] = empty_list()
     has_medical_history: Optional[Union[Union[dict, "MedicalEvent"], List[Union[dict, "MedicalEvent"]]]] = empty_list()
     aliases: Optional[Union[str, List[str]]] = empty_list()
 
@@ -197,7 +199,13 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
             self.has_employment_history = [self.has_employment_history] if self.has_employment_history is not None else []
         self.has_employment_history = [v if isinstance(v, EmploymentEvent) else EmploymentEvent(**as_dict(v)) for v in self.has_employment_history]
 
-        self._normalize_inlined_as_list(slot_name="has_familial_relationships", slot_type=FamilialRelationship, key_name="type", keyed=False)
+        if not isinstance(self.has_familial_relationships, list):
+            self.has_familial_relationships = [self.has_familial_relationships] if self.has_familial_relationships is not None else []
+        self.has_familial_relationships = [v if isinstance(v, FamilialRelationship) else FamilialRelationship(**as_dict(v)) for v in self.has_familial_relationships]
+
+        if not isinstance(self.has_interpersonal_relationships, list):
+            self.has_interpersonal_relationships = [self.has_interpersonal_relationships] if self.has_interpersonal_relationships is not None else []
+        self.has_interpersonal_relationships = [v if isinstance(v, InterPersonalRelationship) else InterPersonalRelationship(**as_dict(v)) for v in self.has_interpersonal_relationships]
 
         if not isinstance(self.has_medical_history, list):
             self.has_medical_history = [self.has_medical_history] if self.has_medical_history is not None else []
@@ -567,6 +575,32 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
         super().__post_init__(**kwargs)
 
 
+@dataclass
+class InterPersonalRelationship(Relationship):
+    _inherited_slots: ClassVar[List[str]] = []
+
+    class_class_uri: ClassVar[URIRef] = PERSONINFO.InterPersonalRelationship
+    class_class_curie: ClassVar[str] = "personinfo:InterPersonalRelationship"
+    class_name: ClassVar[str] = "InterPersonalRelationship"
+    class_model_uri: ClassVar[URIRef] = PERSONINFO.InterPersonalRelationship
+
+    type: str = None
+    related_to: Union[str, PersonId] = None
+
+    def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
+        if self._is_empty(self.type):
+            self.MissingRequiredField("type")
+        if not isinstance(self.type, str):
+            self.type = str(self.type)
+
+        if self._is_empty(self.related_to):
+            self.MissingRequiredField("related_to")
+        if not isinstance(self.related_to, PersonId):
+            self.related_to = PersonId(self.related_to)
+
+        super().__post_init__(**kwargs)
+
+
 @dataclass
 class EmploymentEvent(Event):
     _inherited_slots: ClassVar[List[str]] = []
@@ -667,6 +701,17 @@ class FamilialRelationshipType(EnumDefinitionImpl):
         name="FamilialRelationshipType",
     )
 
+class NonFamilialRelationshipType(EnumDefinitionImpl):
+
+    COWORKER_OF = PermissibleValue(text="COWORKER_OF",
+                                             meaning=FAMREL["70"])
+    ROOMMATE_OF = PermissibleValue(text="ROOMMATE_OF",
+                                             meaning=FAMREL["70"])
+
+    _defn = EnumDefinition(
+        name="NonFamilialRelationshipType",
+    )
+
 class GenderType(EnumDefinitionImpl):
 
     _defn = EnumDefinition(
@@ -763,6 +808,9 @@ class slots:
 slots.has_familial_relationships = Slot(uri=PERSONINFO.has_familial_relationships, name="has_familial_relationships", curie=PERSONINFO.curie('has_familial_relationships'),
                    model_uri=PERSONINFO.has_familial_relationships, domain=None, range=Optional[Union[Union[dict, FamilialRelationship], List[Union[dict, FamilialRelationship]]]])
 
+slots.has_interpersonal_relationships = Slot(uri=PERSONINFO.has_interpersonal_relationships, name="has_interpersonal_relationships", curie=PERSONINFO.curie('has_interpersonal_relationships'),
+                   model_uri=PERSONINFO.has_interpersonal_relationships, domain=None, range=Optional[Union[Union[dict, InterPersonalRelationship], List[Union[dict, InterPersonalRelationship]]]])
+
 slots.in_location = Slot(uri=PERSONINFO.in_location, name="in location", curie=PERSONINFO.curie('in_location'),
                    model_uri=PERSONINFO.in_location, domain=None, range=Optional[Union[str, PlaceId]])
 
@@ -859,3 +907,9 @@ class slots:
 
 slots.FamilialRelationship_related_to = Slot(uri=PERSONINFO.related_to, name="FamilialRelationship_related to", curie=PERSONINFO.curie('related_to'),
                    model_uri=PERSONINFO.FamilialRelationship_related_to, domain=FamilialRelationship, range=Union[str, PersonId])
+
+slots.InterPersonalRelationship_type = Slot(uri=PERSONINFO.type, name="InterPersonalRelationship_type", curie=PERSONINFO.curie('type'),
+                   model_uri=PERSONINFO.InterPersonalRelationship_type, domain=InterPersonalRelationship, range=str)
+
+slots.InterPersonalRelationship_related_to = Slot(uri=PERSONINFO.related_to, name="InterPersonalRelationship_related to", curie=PERSONINFO.curie('related_to'),
+                   model_uri=PERSONINFO.InterPersonalRelationship_related_to, domain=InterPersonalRelationship, range=Union[str, PersonId])

tests/test_loaders_dumpers/test_rdflib_dumper.py

@@ -8,12 +8,10 @@
 from rdflib import Namespace
 
 from linkml_runtime import MappingError, DataNotFoundError
-from linkml_runtime.loaders import json_loader
 from linkml_runtime.dumpers import rdflib_dumper, yaml_dumper
 from linkml_runtime.loaders import yaml_loader
 from linkml_runtime.loaders import rdflib_loader
 from linkml_runtime.utils.schemaview import SchemaView
-from linkml_runtime.utils.schemaops import roll_up, roll_down
 from tests.test_loaders_dumpers import INPUT_DIR, OUTPUT_DIR
 from tests.test_loaders_dumpers.models.personinfo import Container, Person, Address, Organization, OrganizationType
 from tests.test_loaders_dumpers.models.node_object import NodeObject, Triple
@@ -61,6 +59,29 @@
     personinfo:age_in_years 33 .
 """
 
+enum_union_type_test_ttl = """
+@prefix P: <http://example.org/P/> .
+@prefix personinfo: <https://w3id.org/linkml/examples/personinfo/> .
+@prefix sdo: <http://schema.org/> .
+@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
+@prefix famrel: <https://example.org/FamilialRelations#> .
+
+P:001 a sdo:Person ;
+    sdo:email "[email protected]" ;
+    sdo:name "fred bloggs" ;
+    personinfo:age_in_years 33 ;
+    personinfo:has_interpersonal_relationships [ 
+      a personinfo:InterpersonalRelationship ;
+      personinfo:type famrel:70 ;
+      personinfo:related_to P:002 
+    ] ,
+    [ 
+      a personinfo:InterpersonalRelationship ;
+      personinfo:type "BEST_FRIEND_OF" ;
+      personinfo:related_to P:003 
+    ] .
+"""
+
 blank_node_test_ttl = """
 @prefix personinfo: <https://w3id.org/linkml/examples/personinfo/> .
 @prefix sdo: <http://schema.org/> .
@@ -174,6 +195,27 @@ def test_unmapped_predicates(self):
         self.assertEqual(str(person.gender), "cisgender man")
         yaml_dumper.dump(person, to_file=UNMAPPED_ROUNDTRIP)
 
+
+    def test_any_of_enum(self):
+        """
+        Tests https://github.com/linkml/linkml/issues/1023
+        """
+        view = SchemaView(SCHEMA)
+        # default behavior is to raise error on unmapped predicates
+        person = rdflib_loader.loads(enum_union_type_test_ttl, target_class=Person,
+                                schemaview=view, prefix_map=prefix_map)
+        self.assertEqual(person.id, 'P:001')
+        self.assertEqual(person.age_in_years, 33)
+        yaml_dumper.dump(person, to_file=UNMAPPED_ROUNDTRIP)
+        cases = [
+            ("P:002", "COWORKER_OF"),
+            ("P:003", "BEST_FRIEND_OF"),
+        ]
+        tups = []
+        for r in person.has_interpersonal_relationships:
+            tups.append((r.related_to, r.type))
+        self.assertCountEqual(cases, tups)
+
     def test_unmapped_type(self):
         """
         If a type cannot be mapped then no objects will be returned by load/from_rdf_graph